Project GEMINI
by Tye22
Summary: A discovery made by EDI pertaining to a deserted Cerberus research facility proves to be quite the shocker to the crew, especially Kaidan. M!ShepxKaidan, M!ShepxLiara. Rated M for future chapters.
1. Chapter 1

**A/N: Ok so I finally got to play Mass Effect 3 and I loved every moment of it... right until i reached the ending. Thats when I blew a fuse... But anyway I'm not going to rant on about that right now. -deep breath-**

**My main M!Shep that I've been preparing for ME3 romanced Liara in the 1st one and stayed faithful to her in the 2nd one but when I reached the 3rd one something odd happened. The whole flirty thing going on between Kaidan and Shepard really grabbed my attention so in my second play-through I dumped Liara and romanced Kaidan and it was pretty cool.**

** Anyway, to the point.**

** An idea for a fic started to form in my mind where Shepard is faced with an affection for Kaidan but has a hard time showing it because Kaiden is all broody and professional in ME 1. Then after Kaidan's asshole move on Horizon, Shepard finally decides to move on and starts something with Liara during their time together hunting the Shadow Broker. (YES, my Shepard is bi-sexual...) **

**This is bad news for Kaidan as he finally decides to confess his love for the Commander in ME3, but is basically rejected because of Shepards growing feelings for Liara. So cue sexual tension! (I think you can safely assume that there will be some SLASH in the future)**

**Soon after this EDI picks up an interesting communication from Cerberus and things get complicated from there on in. You'll have to read the fic to find out ;P**

** -bleh- sorry for blabbing so much...**

**Enjoy (hopefully) the fic and feel free to comment (constructive please...) or praise (if you liked it :D ).**

* * *

Kaidan chuckled as he shook his head.

"Glad to see you haven't changed that much, Joker." He said as he turned to leave.

"See you, Major." The pilot called as he walked away. It was nice to be around friends again, Kaidan thought. He walked down the corridor lined with monitors and control systems, his eyes following the tiny lights that flickered on the walkway. Slowly his smile faded and his mind drifted to a faraway place filled with recent memories. He was so wrapped up in his own thoughts that he didn't notice where he was going and walked straight into Specialist Traynor. He grunted loudly as they collided.

"Oh, Major Alenko! I'm so sorr-" she began but Kaiden cut her off with a smile.

"Hey, don't worry about it. It was totally my fault." He said with a grin, "Should pay more attention to where I'm going."

Traynor gave him a small smile in return.

"You seem troubled, Major. Everything ok?"

Kaidan hesitated a moment. Traynor caught this and tilted her head, narrowing her eyes slightly. When he seemed at a loss for words she reached out and touched his shoulder.

"Hey, it's ok if you don't want to talk about it. I understand."

Kaidan, who had been staring at the floor, raised his head and grinned apologetically. "Thanks, Samantha. For understanding." She smiled and squeezed his shoulder before dropping her arm.

Kaidan smiled one last time before making his way to the elevator. He was just about to step inside when Samantha called out to him.

"Major? Can I ask you a favour?"

Kaidan turned. "Sure. What is it?"

She turned back to her console and picked up something that lay next to it. She walked over to him briskly and held out data pad.

"This is a summary of recent Cerberus comm chatter that EDI picked up. I've been meaning to take it to the Commander but he has been up in his cabin all day and I don't want to intrude. You're good friends with him so I was hoping you'd rather go up there to pass this along."

Kaidan was momentarily surprised, but reached out to take the data pad.

"I hope it's not too much trouble?"

Kaidan smiled at her reassuringly, though the smile never reached his eyes.

"It's not a problem. I'll take it to him right away."

"Thank you, Major."

Kaidan nodded and stepped back into the lift. Traynor watched him as the doors slid shut and at the last moment she could swear she caught a glimmer of pain in his eyes.

* * *

The steady humming of the elevator came to a sudden stop and with a slight hiss the doors slid open. Kaidan slowly stepped out onto the top level of the Normandy. He slowly made his way to the door of Shepard's cabin but stopped just before it. He hadn't spoken to the Commander since their talk on the Citadel. Kaidan winced as he recalled Shepard's conflicted expression when he had confessed his feelings for the Commander. He shook his head as he recalled the way Shepard had struggled to find the words to let him down as softly as possible.

"_I... I don't know what to say... Kaidan, I- It's just that... I think I've found someone..." _

He let out a pent up breath before reaching forward to open the door. He looked up as it opened to find Shepard and Liara in a tender embrace. His heart sank even lower.

Startled by the sudden noise, the two broke apart. Liara straightened her outfit and Shepard wiped off the lipstick on his cheek with the back of his hand. It left a faint mark there.

Kaiden coughed awkwardly and looked at the floor. He was about to turn away when he remembered the actual reason for his visit and held up the data pad.

"Um, Samantha, Specialist Traynor, asked me to bring you this. It's about Cerberus activities." He walked forward briskly and passed the pad to the Commander.

"I- I'm sorry for just barging in." He said and made to leave but a hand on his arm held him back.

"It's quite alright, Kaidan. I was just leaving anyway." Liara said and moved to walk past him. She turned briefly to glance back at Shepard before stepping out of the cabin. The door hissed shut after her.

"Commander, I-" Kaidan began but Shepard stopped him with a raised hand.

"There's nothing to be sorry about, Kaiden." He said and smiled warmly. He then looked down at the data pad and started scanning through the report, his blue eyes darting from side to side as he did so.

"Project Gemini?" he thought out loud.

"Yes, it's a research project that Cerberus has been working on for the past two and a half years. It's apparently very high priority and top secret. Even EDI had a hard time picking up any intel."

"So what happened? Why has she suddenly caught something on it now?"

"The facility want dark a few days ago. Every recon team Cerberus has sent in hasn't made it out. EDI intercepted a transmission about it this morning. She, along with Specialist Traynor, has been decoding it all day and they have come up with a location."

Shepard thought it over for a while before putting the data pad down.

"Tell Joker to plot a course. Grab your gear and tell EDI to get ready too. She'll be a big help in a Cerberus facility."

"Aye, Commander." Kaidan said and made his way to the door. He stopped however when Shepard said his name very softly.

He looked back at the Commander to find the man looking at him in an odd way.

"Kaidan, I'm sorry you had to see that..."

Kaidan grinned slightly and And looked over at the Commander. The smudge on his cheek was still quite visible and it made Kaidan look away.

"Commander..."

Shepard gave him a sad smile.

"You took too long, you know. I waited a long time but you never made any moves, never sent any signals... And after Horizon... I moved on. And Liara..." Shepard grew silent as he ran out of words to say. He looked at his shoes instead.

"Then why have you been sending me signals now? I've seen the way you look at me sometimes before quickly glancing away. I just thought that-" Kaidan stopped himself. "Just forget about it, Shepard. It wasn't meant to be." Kaidan said with a smile even though he was wincing on the inside. All he wanted to do now was to get as far away from this cabin as possible. He looked up to see Shepard looking at him in a truly confused and conflicted way.

He exhaled deeply and turned, making his way out the door. He heard footsteps following him but he didn't stop. He reached the lift and pressed the button that would take him down to the CIC. He turned around to find Shepard blocking the elevator door. The lift beeped with annoyance at the obstruction.

"What do you want, Commander?" Kaidan asked in an exasperated tone.

Shepard stared at him a moment longer before stepping forward into the elevator and pulling the Major closer.

"I-I honestly don't know." He whispered before leaning down slowly.

Kaidan tensed as the Commander's lips drew closer. He was about to lean into the kiss when his eyes caught the smudge on Shepards cheek. He pulled away swiftly.

"Shepard..." he whispered and shut his eyes tightly, taking in a deep breath. After a moment he looked up again and softly pushed Shepard backwards out of the lift. He reached up with his other hand to wipe the remaining lipstick of the Commander's face. His touch lingered a bit longer that he had planned though. When Shepard reached up to take his hand he pulled away and stepped back into the lift.

Their eyes met just before the doors closed. Kaidan saw a flicker of hurt in those bright blue eyes, the same hurt that he imagined was flickering in his own.

* * *

"I'm detecting an absence of life on the station, Shepard. There is nothing here." EDI said as they turned yet another corner. So far nothing had seemed out of place in the station, except obviously for the lack of personnel or any form of security. EDI did however pick up an unusual amount of Element Zero present in the air. Shepard had to admit that the atmosphere inside the station did seem a bit hazy.

"I would suggest keeping your helmets on for the duration of our investigation." EDI advised. Kaidan nodded his agreement, as did Shepard.

After another 20 minutes of searching for a hint as to what had happened here, Shepard finally stopped.

"EDI, are you sure there is nothing here?"

EDI nodded. "I have scanned the security systems multiple times and I detect no faults. There is effectively no evidence to suggest what took place here. All information pertaining to the nature of Project Gemini has been scrubbed from the system as well."

Shepard sighed. "Scan one more time. Just to be sure."

"Very well." EDI said before taking on a blank look and standing completely still. After a few moments she tilted her head slightly to the side as if she was confused.

"What is it, EDI?"

"I'm detecting a faint heat signature coming from up ahead. I believe it is located directly in the centre of the station. Shepard... It wasn't there a moment ago."

"It's the first lead we've found in this place so let's go take a look." Shepard said and raised his gun. "If there's trouble, we'll be ready."

EDI nodded and took the lead. After heading up a few levels and taking a couple of turns they finally reached a large door. It was locked.

"EDI, see if you can get that door open."

"Right away, Shepard." The AI said and proceeded to hack the door.

"Hey Kaidan? Does the air feel denser to you?" Shepard asked as they waited.

"It feels a little tight, yes." Kaidan agreed.

"And your biotics? Feel anything odd?"

Kaidan hesitated. "I have been feeling... I don't know, stronger? Since we came here."

Shepard nodded. "I feel it too... Something strange is going on here."

The door suddenly beeped and slid open to reveal a spacious laboratory. The group moved forward with caution, weapons raised. EDI made her way to a console on the other side of the room, Shepard and Kaidan watching for trouble.

"There is no one here." EDI stated as she worked. Neither of the men let down their guard though.

"Better safe than sorry, EDI." Kaidan said as he walked further into the room.

Shepard crossed over to the AI to see what she was doing. She paid him no notice as she tapped away at the console. Files flew across the screen so fast Shepard could barely read what they said. He did however catch his name a few times as well as mention of a Subject Alpha.

"This console has not been completely scrubbed. I am accessing the data remaining on Project Gemini and downloading it directly to the Normandy. "

"I see my name in these files. What's going on here EDI?" Shepard asked the humanoid AI but before she could respond they were interrupted by a loud gasp coming from the other side of the room.

"Shepard!" Kaidan called. "Shepard, you have to see this!"

The Commander left the AI to finish her work while he swiftly made his way to the side of the room where Kaidan was standing in front of a large glass tank. It was filled with a strange blue fluid and glowed with a soft light.

"What is it, Kaidan? Did you find anything?" he asked as he came to a stop next to the Major.

Kaidan turned to face him, his eyes wide but he said nothing.

"Kaidan? What-" he began but stopped when he caught movement in the tank. He turned to look at it more clearly.

"Did you see something in there?" he asked.

Kaidan nodded slowly. "Yeah..."

"What?" Shepard asked loudly, growing frustrated. He leaned in close to the tank to try and see through the hazy blue liquid.

"It- It's... You, Commander..." Kaidan said softly and glanced back into the tank.

"What the fuck are you talking abou-" Shepard began but stopped as he finally caught sight of what had the Major so spooked. There, right in front of him in the hazy tank, floated Commander John Shepard.

* * *

**A/N: Keep in mind this is my first Mass Effect fic, so don't kill me if it sucks...**

**If you have any questions, please ask in a review or PM me if you like.**

**Thanx for reading. xx**


	2. Chapter 2

**OK, got a really good reaction to this fic so here is the update :D**

**Quick pic I drew of Shepard if you're interested - http colon slash slash thevoicesmustburn dot deviantart dot com slash # slash d4yfbff**

**Enjoy the fic! And let me know what you think ;P**

* * *

"This isn't possible..." Shepard whispered and reached forward to press his hand on the glass. It was warm to the touch and made the tips of his fingers tingle. As he drew away a small spark seemed to jump from his hand to the tank. A surge of electrical energy swept through the murky fluid, crackling around the body suspended in it.

A loud thud sounded from somewhere below them. Slowly the fluid in the tank began draining away. Kaidan gasped and stepped back, but Shepard didn't even flinch. His attention was focused on the activity inside the tank.

"It seems as if the release protocols have been activated." EDI stated from where she still stood, tapping away at the console.

"But we didn't do anything." Kaidan whispered.

"I am trying to pinpoint the origin of the release command. Shepard, what course of action do you wish us to take once the tank is drained?"

The Commander didn't respond. EDI repeated her question but still she was met with silence. Kaidan stepped forward and lightly touched Shepard's shoulder.

"Commander, what do we do?"

John stared up at his own face for a moment longer before finally opening his mouth to speak.

"We bring 'him' with us. EDI, Liara and doctor Chakwas must analyse everything we've found here. We need all the info we can get on Cerberus and if there are more of 'these' we need to know where and, if possible, why they were created."

"Right, Commander."

"EDI, any suggestions on how to transport, um, well 'me' back to the Normandy?"

The AI turned away from the console, apparently finished with her work and made her way to the two men.

"Shepard, I have uncovered a video file that may reveal what happened here." She said as she activated her omni-tool and held it up for both men to see.

The scene showed a group of people, probably scientists judging by the lab coats and data pads, discussing various readings and info gathered from their tests on the Shepard clone. One of them pointed out that Subject Alpha was showing off the chart Element Zero levels and that it could be potentially dangerous if the power levels kept rising at the rate that they were. One of his colleagues scoffed at him, stating that there was nothing to worry about and that the high eezo levels would equalize soon after Alpha reached maturity.

The scene then jumped to a more recent entry. The scientist who had scoffed his colleague was shown entering the lab where they now stood. He walked over to the console where EDI had been working and started tapping away furiously. Every now and then he would glance around to check if anyone was there. A disembodied voice suddenly announced that eezo levels were multiplying at an enormous rate. The scientist smiled, seemingly elated at what he had done. His joy was short-lived however as red lights started flashing on the console and a loud hissing noise escaped from the other side of the room, possibly from the tank. The scientist looked back at the console, swore and then tapped away again. The hissing grew louder, making the scientist look frantically back and forth between the console and the tank. The disembodied voice rang out again, this time in warning.

The scientist was sweating now, cursing as he worked frantically. A crackling sound filled the air and sparks shot from the console, making the scientist fall back in shock. He sat there staring at the console for a few seconds before slowly turning his gaze in the direction of the tank as a blue glow radiated from within. The scientist closed his eyes and whispered something inaudible. Suddenly a bright blue light flashed through the room, temporarily cutting of the video file. As the image returned a few moments later, it was finally revealed what had happened to the scientists on the station.

"It appears as if an enormous wave of biotic energy swept through the station and vaporized the staff." EDI said as they watched the scientist's body crumbled to dust, dissipating into the air.

"That's incredible..." Kaidan whispered and glanced back at the clone.

Most of the liquid had already drained away; leaving the body slumped against the glass. A hiss sounded just as the glass started to slide away. Reacting without thinking, Kaidan jumped forward and caught the unconscious figure before it fell forward and hit the ground.

"You're surprisingly light, Commander." Kaidan remarked as he hoisted the clone into his arms, cradling him like a child.

"Nice catch, Major." Shepard said with a small smile, but his expression grew cold as his eyes fell on the clone. "But remember one thing... THAT is not me."

"Of course, Commander."

Shepard nodded sharply and turned to EDI.

"Did you get all the data? Can we leave?"

The AI nodded.

"I have downloaded all salvageable data and forwarded it to the Normandy."

Shepard glanced over his shoulder at Kaidan before moving towards the main door.

"Let's go then."

"Right behind you, Shepard."

* * *

News spread through the Normandy like wildfire. Soon everyone was talking about the extra passenger they had picked up and most wanted to catch a glimpse of him. Because of this Shepard had restricted access to the med-bay to give the doc some space to run her tests and diagnostics. Liara stepped in every now and then to assist, while EDI analysed the data she had recovered.

Shepard also asked if there were volunteers to watch over the clone, in case there was trouble. He was far too busy to worry about it in any case. Traynor had received Intel on another matter that required his immediate attention. Kaidan stepped up rather eagerly to fill the position. Shepard found this odd, but said nothing.

He called Joker up and told him to plot a course. He then let James and Garrus know that they would be joining him on this mission and that they should suit up. After checking his armour and weapons he decided to catch a few minutes of sleep and headed up to his quarters, hoping he wouldn't be plagued by nightmares of the galaxy burning up around him.

* * *

Kaidan sat in an empty chair, going through some data he picked up at the Spectre terminal last time they were at the Citadel. Chakwas had left a while ago, saying she needed a break, leaving Kaidan alone with the clone.

Kaidan would find himself glancing at the sleeping figure every now and then, his eyes taking in every feature. He noticed that the clone wasn't as muscled as the Commander, but that was understandable, seeing as you're not too active when floating around in a tank.

His eyes travelled up to the face and he smiled slightly as he took in the peaceful expression of the man who looked like the man he yearned for. The clone didn't have the buzz cut the Commander sported; instead his hair grew out thick and dark. It wasn't long, but there was definitely more of it. Kaidan found it strange to see the Commander's face with longer hair. The slight difference in appearance did nothing to lessen his longing. If anything it only made it worse.

However, the longer he stared the more his longing turned to suspicion. This man wasn't Shepard. It was a copy, created by Cerberus. Its purpose was most likely something sinister as nothing truly good ever came from that organisation, no matter what they said.

Kaidan found that he was glaring at the clone now, the crease in his forehead starting to ache. He sighed loudly and got up. Slowly he paced the length of the med-bay, his hands locked behind his neck.

He was concentrating so hard that he almost walked into the door a couple of times. As he passed the sleeping clone for the hundredth time, he heard a small moan.

He froze and glanced down at the figure. He was moving, twitching slightly, his eyes darting left and right behind his lids. Kaidan reached for the pistol at his side and flared up a biotic barrier, just in case.

The clone twisted and turned; a pained expression on his face. Concern flashed through Kaidan. Even though it wasn't technically the Commander, this man still looked like him. Kaidan was conflicted. What would he do if the clone attacked?

He didn't have a long time to think it over though because the next thing he knew, the clone drew in a deep, gasping breath and sat up straight. His eyes flew open.

Kaidan stood there, too stunned to act, staring into the deepest purple eyes he had ever seen.

* * *

**Okee, so it's not the longest chapter I've ever written, but that's all I had time for... (duty calls)**

**Decided to change the appearance of the clone ever so slightly, cause the people on the Normandy are gonna get confused I think...**

**The vaporizing scientists thing was partly inspired by the way Meredith from DA2 kinda becomes a lyrium statue and then crumbles... **

**Anyway, hope it was enough to keep you busy for now and check in soon for another update.**

**P.S: I'm addicted to reviews, so feed me plz!**

**Thanx for reading xXx **


	3. Chapter 3

**Sorry for the extended period of silence *sheepish grin***

**Here is a short chapter update, just to wile away the time or whatever.**

**Enjoy ;P**

* * *

"Kaidan? What happened? Where-" 'Shepard' began but stopped when he noticed the shock on the other man's face. He was about to ask what was wrong when he suddenly doubled over as extreme pain shot through his body. Kaidan stood absolutely still for a few seconds until the pained moaning and gasping coming from the shuddering figure in front of him proved to be too much.

"Easy does it, um Commander. Just lay back, you've um, been through a lot." Kaidan said as he slowly pushed the clone back against the bed.

'Shepard' winced as the pain continued, a cold sweat breaking out over his body, making him shiver. Kaidan frowned at the scene before him, still conflicted as to how he should be treating the clone. The way he had looked at him when he first opened his eyes, the recognition in his voice, the way he had said his name... All of this was proving way to confusing. It took him a few more moments to reach a decision.

He walked over to the nearby cabinet and quickly sorted through the bottles and boxes until he found what he needed. Mixing the contents of the bottle he found with a cup of water that stood next to the bed, he sat down and offered it to the clone.

"Chakwas always gives me this when my L2 starts acting up. It tastes like piss but it really helps."

'Shepard' reached over with a shaking hand and accepted the cup. He took a sip, pulled a face and nearly spit it out but eventually swallowed it. Kaidan grinned before urging him to finish the rest. Soon the shivering had subsided and 'Shepard's' breathing was back to normal.

"That stuff really works." 'Shepard' said in a hoarse voice, closing his eyes.

"That it does."

'Shepard' grinned, his eyes still closed. He lay still for a moment before he sat up straight again with such speed that Kaidan nearly fell off the edge of the bed.

"The attack! What happened?"

"Shepard, what are you talking about?"

"Explosions, rushing to save everyone, saying goodbye to-" he trailed off for a moment before continuing, "...then not being able to breathe, crushing darkness..." he finished, a distant look on his face.

Kaidan's eyes grew large as he realized what the clone was going on about. He had all of Shepard's memories up until the Collector attack almost three years ago. This complicates things...

'Shepard' looked up into eyes. His brows wrinkled together.

"Kaidan?"

"Yeah? Sorry I was just," he paused. "I'll be right back. Just have to go check on something." He said and walked over to the door.

"You just relax, Commander." He said before the door slid shut behind him.

He could hear a muffled 'ok' from the other side. Kaidan sighed loudly and leant against the wall for a few moments, his eyes closed. He didn't know how to handle the situation. His first thought was to go get John but he was still ashore with Garrus and Vega. Eventually he decided to go ask Liara what to do.

He found the scientist glued to one of the many monitors that lined the walls in her quarters. She briefly looked up to see who had entered but said nothing, furiously typing away at the console. Glyph, the Asari scientists VI assistant hovered over to him.

"Dr. T'soni will be with you in a moment, Spectre Alenko."

Kaidan nodded. It was still a strange thing to be called Spectre.

He decided to lean against the wall as he waited. Finally Liara stood and walked over.

"Sorry about that, Kaidan." She said with an apologetic smile. "I was in the middle of some important work regarding the Crucible that simply couldn't wait."

"That's ok." he said with a small grin.

"What did you want to see me for?"

"It's well, um the Commander."

Worry momentarily flashed across her face.

"What? Did something happen?"

Kaidan caught the concern in her voice.

"Oh, no I'm sure John is fine. It's the 'other' one I'm referring to."

Liara frowned.

"The clone, you mean?"

"Yes. He's awake."

"Is he violent?"

"No, just confused. I gave him some pain meds. He's resting now."

"So what's the problem exactly?" Liara asked.

Kaidan paused a moment before answering.

"He seems to have all of Shepard's memories up until the Collector attack. Three years ago."

Liara stood silently taking in the info.

"Liara, He thinks HE is the real Shepard. When he opened his eyes, the look he gave me..."

The scientist looked up at him.

"Kaidan. He might seem identical, but he isn't."

Kaidan sighed.

"I know... what do we do now?"

"I'm not sure. We'll have to wait for John to get back. For now just keep an eye on him."

Kaidan nodded. He had been hoping she would be of more help but he guess she was just as unsure as he was. Turning, he bade both her and Glyph goodbye and headed back to the med bay.

* * *

The clone smiled as he entered carrying a tray.

"Thought you might be a bit peckish after-" he trailed off for a moment. "Chef whipped this up a while ago. Wasn't too bad." He said, twisting the conversation in a different direction.

'Shepard' sat up as he approached.

"Thanks. I was just about to call someone for some room service." He said with a grin.

Kaidan placed the tray on the clone's lap and took a seat.

"It would be best if you stayed here for a while..."

'Shepard' gave him a side long glance as he chewed.

"Okay..." he said slowly as he watched Kaidan's face.

"Kaidan, what's wrong?"

Kaidan looked down at the floor for a moment before speaking.

"Commander, there have been a few developments since you last opened your eyes."

'Shepard' eyed him suspiciously.

"What kind of developments?"

"Well..." Kaidan began, but before he could say anything else, the door slid open and in strode Shepard.

"Good, it seems I'm finally awake."

Kaidan sighed as he looked from the one Shepard to the other. The clone's eyes were wide as he stared at the approaching figure. He glanced back at Kaidan, his mouth hanging open in shock.

"You're not the most tactful person in the galaxy, are you?" Kaidan asked the Commander came to a stop on the opposite side of the bed.

"No, I guess not." He replied with a grim smile before turning his attention to the figure on the bed.

"We haven't been properly introduced." He said holding out his hand. "I'm Commander Shepard."

The clone looked from his hand to his face. Slowly he reached out to take the offered hand. Then everything was a blur. In a flash the clone had flipped Shepard over the bed, lunging after him. There was a momentary struggle but the element of surprise tilted the conflict in the clones favour. Soon the clone had Shepard pinned to the floor, his own pistol pushing into his temple.

"No," the clone breathed. "I'm Commander Shepard."

* * *

**Ok, I have a few questions...**

**Do you like the direction it's going in? Any changes you'd like me to make? Suggestions please?**

**Also, I don't want to keep on calling the clone 'Shepard' because its gonna get confusing eventually.**

**Please review! I'd love to hear your thoughts.**

**P.S: Sexy time suggestions?**


	4. Chapter 4

**Ok, finally got around to writing again (I'm embarrassed to say it's not that big of an update)**

**I just had a little burst of inspiration and this is what resulted.**

**Enjoy! Any comments/advice welcome!**

* * *

Shepard chuckled as the gun pressed harder against his head.

"He's got quite the temper." He said with a grin, not seeming to care about the seriousness of the situation.

"What's going on here?! Why do you look like me?" the clone demanded.

"Why do YOU look like ME, you mean." Shepard said calmly.

The clone looked about ready to explode.

"Commander, I don't think it's wise to carry on in this way."

"You were always a bit of a spoil sport, Kaidan." The commander said with a sigh.

Shepard tried slowly to get up but the clone was stronger than he was he noted with slight surprise. The clone did not say a word. He only glared intently at the commander. Shepard looked over at Kaidan.

"Would you mind?"

Kaidan frowned before walking over. He moved slowly, not wanting to appear as a threat towards the clone. He was afraid what might happen if he was startled. He steadily reached out and placed his hand on the clone's shoulder. Purple eyes met his.

"Shepard... you're a... a clone." Kaidan said softly as he looked deep into those confused eyes.

The fire in the clone's eyes faltered, replaced by shock. He briefly looked back down at the man who wore his face before slowly stumbling to his feet, dropping the gun. Shepard huffed as he stood, rubbing his left shoulder to try and alleviate some of the pain that had been caused by his hard impact to the ground.

"How can I be a clone?" 'Shepard' asked as he looked back at Kaidan. "I'm Commander Jonathan Shepard. Always have been." The pain and confusion in his voice made Kaidan ache.

Kaidan sighed softly.

"We found you in an abandoned Cerberus research station. You're part of what they called Project Gemini."

The clone looked away. Kaidan could see he was struggling with this news.

"Why would Cerberus want to create a clone?"

"We think it was one of their back-up plans." Shepard said from where he stood.

"For what?"

"For bringing me back."

"From where?"

"Are you really that dense?" The commander snorted.

Kaidan turned to glare at him.

"Are you just about done, commander?"

The authority in Kaidan's voice made the commander's attitude disappear. For a moment he looked a bit sheepish.

"This could have gone completely different if you hadn't decided to be such a dick. A while ago you were in a similar situation, or did you forget? From what I hear, you weren't so chuffed at what had happened either, but instead of trying to help him," Kaidan said pointing at the clone, "you act like a dipshit just to show that your gun is bigger than his."

Shepard, who was looking like a kid being yelled at right up until Kaidan made the 'gun' comment, smirked.

"So, you think my 'gun' is bigger that his?"

Kaidan gave him a blank look.

"Really, commander?"

Shepard chuckled.

"Ok fine, I'll admit that that might have been a dick move. But when I walked in and saw you two-" he trailed of suddenly, as if he realised he had said that out loud. Kaidan raised his eyebrow at this and felt his heart beat a bit faster. Was Shepard jealous? Before he could ask, EDI's voice rang out over the comm-system.

"Commander?"

Both Shepard and the clone looked up.

"Yes EDI?"

"Commander, Liara and I have been talking and we want to make a suggestion."

"Um, sure."

"After thorough analysis we have determined that the clone-" she stopped suddenly as if she had said the wrong thing. Kaidan smiled at this human reaction. EDI was becoming more 'alive' by the day.

"Forgive me, I did not mean to sound insensitive."

It took the clone a few moments to realise that she was talking to him.

"... it's ok um EDI? That's what I am, I guess..." the clone said blankly.

EDI remained silent for a moment before continuing.

"We have concluded that project Gemini was not fully completed, the fact that he only has memories up until the accident further proves this. We can thus assume that further tampering with his mind did not take place. He does not seem to be a Cerberus agent then."

"Your point, EDI?"

"Her point," Liara interrupted , "is that with two Shepards on board we have double the shot at winning."

"Liara, are you-"

"You saw what he did to those scientists. His biotic powers are extraordinary." Liara said, appealing to the side of the commander that couldn't resist turning away a powerful ally.

Shepard paused.

"You have a point there..."

"If anything, you could send him on the missions you don't feel like doing." Joker added to the conversation.

The clone looked slightly flustered, but smiled at the sound of Jokers voice.

"Glad you're still here, Joker." He said, forgetting for a moment that he was the clone.

"Where else would I be, Comman- Um I mean, Jonathan. Why Jonathan? I thought your name was just 'John'."

"It's always been Jonathan." The clone said confused.

"But my name has always been John." Shepard added.

"Hmmm." Joker mused over the comm line. "At least now there won't be an issue on how to distinguish you two."

Kaidan glared at the comm speaker.

Shepard sighed.

"Fine, he stays... for now."

Kaidan smiled at Jonathan. The man gave him a small smile in return.

"We don't know what the Illusive Man might be up to. I want him under constant surveillance. He is never to be left alone."

"I'll stay with him." Kaidan said a little too quickly.

The commander flashed him another look that added to the 'jealousy theory' while Jonathan gave him a warm smile.

"Very well. He's your problem from now on then." Shepard said sharply before turning towards the door.

Kaidan walked o

* * *

ver to where the clone, no he corrected himself, to where Jonathan sat. He helped the man lay back down on the small bed.

"You should get some rest. You're still a bit drained." He said softly before turning to fetch a glass of water.

"Kaidan?"

"Yep?"

"Thank you, for staying with me."

Kaidan gave him another wide smile.

"Where else would I be?"

* * *

John stood outside the med bay, leaning against the wall. Inside he could hear the two men laughing. He scowled at the sound of his own voice coming from inside. Kaidan was too trusting he decided. He just saw a confused lonely man, who coincidentally had the same face as the man he confessed to having feelings for, and didn't see past that and the potential for danger.

Another laugh came from inside. John clenched his fists.

No... That wasn't the real reason he was angry.

He sighed, looked sadly at the door before walking away, the sound of laughter ringing in his ears.

* * *

**Jealous Shep is quite... sexy... I must admit.**

**Anyway.**

**Ok, so I liked all the name suggestions you guys gave me but I didn't quite know how to bring in such a huge name change. 'Jonathan' was quite close to 'John' so that's what i settled on. Also '_Panda' _suggested that I bring in some inconsistencies between the two Shepard's back stories (as in the whole 'spacer, colonist, earthborn/warhero, ruthless, sole-survivor' thing.) which I would really like to bring in. **

**Thanks for all the reviews and follows and favorites and likes and loves and whatever ;P I really appreciate the support!**

**Please feel free to make any suggestions, I'm open for ideas!**

**Stay tuned!**


	5. Chapter 5

**Ok, Update time :D**

**Just want to say thanx for everyone who took the time to review previous chapter and adding this story to favourites and so on. I really appreciate it :)**

**This chapter was quite fun to write, I must say. Was listening to a mix of Madeon, deadmau5, Florence and 30 Seconds to Mars while writing which was quite interesting haha. I didn't have a chance to really go through it again to check spelling and grammar so excuse the mistakes that I'm pretty sure are there. Anyone up for BETA work let me know, it'll be a big help :)**

**I liked the idea proposed by 'HarleyQuinnAddict'. I hope you don't mind that I ran with it :)**

**Also, 'Panda' your little freak out made my day, so thank you very much ;) **

**Anyway, on with the show!**

* * *

The days following were relatively awkward for the entire crew. Although no one seemed to have a direct problem with Jonathan, most people tended to avoid him. This bothered him greatly. It was difficult not being able to speak to people in the same way he had done before or rather was programmed to think he had spoken to them.

The 'clone' thing hadn't completely sunken in yet. He didn't feel like a copy. His memories were too real to have been engineered. The feelings they generated were too intense. The way he felt about Kaidan couldn't be programming either, he was sure of it. Every time the biotic walked in to the room he could feel his heart flutter. He didn't say anything though, instead giving the man a friendly smile. He didn't think Kaidan would ever feel anything for a mere copy. Especially if the 'original' was right there.

His relationship with John was unstable to say the least, particularly in terms of interacting with Kaidan. Whenever John saw the two of them together whether they were having a chat or simply sitting at the same table having lunch his mood would turn sour and he would go out of his way to interfere, sometimes indirectly, but most often taking a hands on approach. His actions were not lost on Kaidan though. The biotic would regularly confront John, this usually leading to a fight breaking out between the two. At the end of one of these fights Jonathan caught a glimpse of John's face as Kaidan turned away to storm off. The initial rage dissipated and was replaced but a look of such anguish that Jonathan could do nothing but stand a stare for a while even after the Commander had left. The raw emotion he had seen that day only served to strengthen his belief that he didn't stand a chance when it came to Kaidan.

He sighed as he sat back in the lounge chair, setting the data pad down next to him. He was trying to go through some data on the Crucible to help Liara but found his mind drifting off. Even though the situation he found himself thrown into was staggeringly overwhelming with the Reaper-War, the Prothean weapon, the new Normandy and his 'creation' he still found himself fretting over Kaidan.

At that moment Kaidan decided to walk in. Jonathan mentally cursed as his pulse rose at the sight of him.

"Napping while on duty are we?"

Jonathan chuckled softly.

"Looks like you caught me."

Kaidan grinned as he walked over to stand in front of the seated man.

"We'll have to take some form of action to ensure it doesn't happen again." He said, lifting his eyebrow and giving a coy smile.

Jonathan laughed this time, inwardly trying to focus on other things but he couldn't help but look at the enticing expression on Kaidan's face.

"Jonathan?" Kaidan asked, waving his hand in front of the man's face.

Jonathan shook himself.

"Sorry about that." He said with a sheepish grin.

Kaidan smiled at him again, warmly this time.

"How's the biotic training with Liara going?"

Jonathan looked at the ground for a brief moment before answering.

"It's progressing, I guess."

"You guess?"

Jonathan sighed.

"I don't quite understand it. I've always been great with biotics. I don't get why now all of a sudden I can barely keep it under control."

Kaidan sat down next to him.

"EDI has a theory. She thinks that because of the elevated strength of your biotics caused by the tampering of those scientists on the Cerberus station, you're not able to control your powers because your memories and skills were programmed to work with more regular levels of biotic strength. It seems to be the most logical explanation."

Jonathan nodded.

"I see."

Kaidan sat looking at him for a few moments before getting up.

"Well, seeing as you don't have any work to do right now," he said with a grin, "why don't we go down to the shuttle bay and practice a bit? I know it's difficult with Liara because she's so busy all the time."

"I'd like that." Jonathan said with a smile.

Kaidan smiled back down at him, extending his hand to pull the man up.

He underestimated the speed with which he did so resulting in the two bumping into each other. Neither moved to step back though, extending the contact. Violet eyes locked onto rich brown ones. They stood completely still for a few moments before Kaidan's face went bright red. He stepped back a bit but caught his boot against the corner of the lounge chair. Jonathan chuckled at awkward stumble that followed.

Kaidan, still sporting a deep shade of red on his cheeks, looked over at Jonathan and gave a small grin.

"Sorry about that. I didn't mean to laugh." Jonathan said apologetically, though he still wore a smile.

"That's ok, Commander. It must have looked pretty funny."

Jonathan gave him another smile, although this one didn't reach his eyes.

"You know, you're the only one who still calls me Commander."

Kaidan's smile melted away.

"Jonathan… I know it's difficult, but you must understand-"

"I know, I know," Jonathan interrupted, "You don't have to tell me."

Kaidan's brows drew together as he regarded the man in front of him with a sad look.

"Hey, even though you aren't the Commander that the rest of the galaxy knows, you'll always be Commander Jonathan Shepared to me."

As Jonathan looked up at the man in slight shock at the sincere comment, he made a decision right then and there. He was going to fight to win the love of this man in front of him, even if that meant going up against himself to do so.

* * *

They found the Shuttle bay empty. This was a bit unusual but they didn't pay it any large amount of attention. Everyone was probably getting lunch. It was about midday after all.

Taking up positions on opposite ends of the bay, the two biotics faced one another.

"Ok, I think we should start with some simple stuff, like barriers maybe?"

Jonathan nodded his agreement.

"You first then. I'll attack with a low level warp."

Jonathan nodded once more before bringing up a shimmering biotic barrier around himself. Kaidan assumed an attack stance. They stood silently like that for a few moments before, with a small popping sound, Kaidan released his warp attack. It hit the barrier with a thud. The field rippled slightly but held.

Jonathan smiled.

"You'll have to do better than that."

"Ok then, get ready." Kaidan called from across the room.

His second attack was packing a lot more force than the first. It hit the barrier with a resounding crack. Jonathan staggered back a step but the barrier held up. Seconds later another warp hit, followed shortly by yet another. The barrier rippled again before flickering as it struggled to absorb the sudden attacks. Jonathan strained, pouring more effort into maintaining the shield. Kaiden let loose another powerful bolt, this one proving too much for Jonathan. The barrier dissipated as the bolt of power hit, the force of the explosion making Jonathan fall over onto his back.

Kaidan chuckled triumphantly from his side of the hanger. Jonathan sat up grinning.

"Wow."

"Hey, I'm impressed. Most barriers would have faded after the second attack but yours held up for quite a while."

"Don't sell yourself short, those attacks were brutal."

"You up for more?" Kaidan asked with a grin.

"Hell yeah. But it's my turn to attack."

Kaidan threw up his own barrier, waiting for Jonathan to attack. The wait seemed a lot longer than it actually was. Jonathans warp field hit the barrier with a loud crack. The shield held, but only barely. Another attack followed, this one slightly stronger. There was another crack followed by a pop as the shield broke.

"See what I meant. Regular shields don't last that long against warp attacks, especially yours. That first shot almost had me." Kaidan said catching his breath.

Jonathan grinned.

"Again?"

Kaidan chuckled before nodding.

"Again."

* * *

Their sparring match went on for what felt like hours. Cortez came back from lunch but he did nothing to interrupt. He simply went to his station and got busy with his own work, occasionally stopping to watch the displays of power. Jonathan and Kaidan made turns alternating between attack and defence, making use of various abilities and maneuvers.

Sweat was trickling in rivulets down Jonathan's back as he prepared a biotic charge. Kaidan had thrown up another barrier to slow the attack and stood poised to dodge should that fail. Both men were breathing heavily.

Flickers of blue light danced around Jonathan as he initiated the fast paced assault. In a flash he darted forward, shattering the shield before him. In another second he was right in front of his target, the man barely having time to blink let alone jump out of the way. With a thud and a groan they collided, landing in a heap on the ground, Jonathan pinning Kaidan's arms to the sides of his head.

"Looks like I win this round as well." Jonathan said with a smirk.

Kaidan struggled in vain to get his arms free. Finally he gave up with a small chuckle.

"Do I get a reward?" Jonathan asked, raising and eyebrow.

Kaidan was momentarily taken about by the suggestive comment. He gazed up into the deep violet eyes that seemed to look inside his soul and felt his initial shock fade away. Acting on impulse he wrenched his arms free, taking advantage of Jonathan's lowered guard and drew the man's face down into a kiss.

Violet eyes went wide for a moment before going half lidded as the kiss deepened. He placed his hands on Kaidan's shoulders and leaned back, pulling them both upright but maintaining the contact. Kaidan steadied himself, letting Jonathan straddle him. Kaiden opened his eyes briefly to see the look of pure lust in Jonathan's. He groaned as Jonathan parted his lips slightly, letting their tongues touch, tentatively at first before forcefully intertwining. The feeling was electric.

Cortez looked up from his work for a moment to see what was causing the two sparring biotics to moan in such a way. He did a double take when he saw why. A small smile crept across his face as he turned away, shaking his head. He was about to head out to give then some privacy when he heard the hiss of the elevator door opening. He turned to see Shepard stepping out. He glanced momentarily at the two biotics before looking back at the Commander. Shepard was about to speak when he followed the direction of the pilot's furtive glance. His jaw dropped.

Kaidan briefly opened his eyes at the sound of the elevator door closing. He took in the sight of the Commander staring at them, Cortez standing of to the side looking like he was about to navigate a minefield. Kaidan gasped and pushed Jonathan away. Confused, Jonathan looked back over his shoulder at whatever was causing Kaidan obvious distress. His eyes widened.

"Shit." He cursed under his breath.

"That's an understatement." Kaidan whispered.

The two men awkwardly stood, neither knowing what to do. John's eyes finally narrowed as he glared at Jonathan. Swiftly he walked towards them clenching his fists. Before either of the men could react, John threw a punch aimed at Jonathans face. He staggered back as the blow hit. The metallic taste of blood filled his mouth.

"What was that for?!" Kaidan yelled.

"He had his hands all over you!" John yelled back.

"Why do you care?!"

"I-" John began but was cut off by a fist colliding with his jaw. The attack was so unexpected that it sent him to the floor. Jonathan sucked in a hissing breath as he shook the hand he had just punched John with. Kaidan stared wide-eyed at the two men, his anger momentarily forgotten.

John stood, spitting out blood. Quick as a flash he aimed another punch; Jonathan blocked it this time before counter attacking. Soon the two were having an all out fight, rolling around on the shuttle bay floor, kicking and punching.

Vega, who had just entered the bay, rushed over along with Cortez and pulled the two apart.

"What the hell is going on down here?!" Vega demanded.

"None of your business Vega." John growled.

"He caught those two making out." Steve said gesturing to Kaidan and Jonathan.

Vega looked over at the pilot.

"Seriously?" he asked.

Steve Cortez nodded, a small smile on his face.

James looked back at the other two men.

"Strangely, I'm not that surprised. Always felt a vibe between you two."

John's face went red.

"That was with ME, Vega! Not this, this copy!"

"But I thought you were banging Liara?"

John opened his mouth to speak but no words came out. Finally he turned away.

"Why are you so jealous, John?" Kaidan asked, placing a hand on the man's shoulder.

"I… I don't know why." He replied in a small voice.

Kaidan felt something tug at his heart at the hurt in Shepard's voice.

"John-" he began but was stopped as Shepard drew his shoulder away from his touch.

"That's Commander to you, Alenko." He said menacingly before storming off to the elevator.

Kaidan straightened at the comment, his feelings of regret and guilt fading in an instant. He turned away as John made his way across the room, looking instead at Jonathan who stood glaring after the retreating figure.

John stepped into the lift and turned to face the group of men watching him, all of them except Kaidan who was looking up at the clone. Kaidan placed his hand on Jonathan's cheek and turned his face towards him. John could see Kaidan lightly touch the cut in Jonathan's lip. He could hear Jonathan whisper that it was nothing before giving him a warm smile. John's glare only deepened.

Kaidan smiled back at Jonathan before briefly glancing over as the lift door started to hiss as it closed. His eyes briefly locked onto the icy blue eyes of the man he had been yearning for all these years. 'Had' being the key word. As those doors slid shut he felt a door inside him slide shut as well. He sighed softly before looking back at Jonathan. At the smile he saw there he felt that as that one inner door closed, another opened.

* * *

**Yay for clone love!**

**I actually feel kinda bad for doing that to John, but oh well... He was the one who decided to be an asshole, not me...**

**So, Love it/hate it? Let me know ;)**

**REVIEWS ARE FOOD FOR MY SOUL**

******(btw, I know that 'Biotic Charge' isn't really an Adept skill, but in this fic lets just pretend that it is.)**


	6. Chapter 6

**Another update!**

**I guess I'm feeling inspired...**

**This chapter is a bit emotional I guess. A bit unexpected as well.**

**Hope you enjoy it anyway ;P**

* * *

Jonathan was stunned to say the least. He had thought his playful suggestion would have been pushed aside, seen as a simple joke. Instead, Kaidan had practically jumped him. When he closed his eyes he could still see that primal glint in Kaidan's eyes. It sent shivers down his spine.

The bruised cheek and cut lip had been worth it. At least, he thought so. After the fight, Kaidan had taken him to see Doctor Chakwas and had left soon after, entrusting the good doctor to keep an eye on him. As if he needed a babysitter. He didn't complain though. He always enjoyed listening to the stories Chakwas had to tell about her past escapades. She was in the middle of one such a tale when John walked in. Apparently he had finally gotten over his pride and come to see the doctor about his own injuries. When he saw Jonathan he froze momentarily, but then seemed to shake himself and proceeded into the Med bay.

"Ah, Shepard. I was wondering when you would stop by." Chakwas said in a tone that reminded Jonathan of a mother about to scold a misbehaving child.

"Yeah well, here I am." John said, not making eye contact with either of them.

"We can chat more later, doctor." Jonathan said, making to stand up and leave.

Chakwas nodded and flashed him a brief smile, but John stopped him with a palm on his chest as he moved past.

"Stay. We have to talk."

Jonathan was slightly taken aback. He hadn't expected John to be the one to instigate the much-needed conversation. He nodded slowly and turned back to the chair he had been sitting in. Chakwas grabbed John by the arm and pulled him over to her equipment. John flinched a few times as she went about her work, complaining whenever the disinfectant stung or when she prodded a bruise.

"Stop being such a baby!" she scoffed, "He didn't even flinch once." She said gesturing towards Jonathan. John scowled.

Jonathan groaned inwardly. As if he needed the doctor's help to antagonize John any further. He briefly glanced over at the Commander. The scowl had softened. He now wore a placid expression as he looked over the doctor's shoulder at Jonathan. Their eyes met briefly before both men looked away.

"Awkward…" Jonathan whispered to himself.

Minutes ticked by until the doctor was finally done. She dumped the swabs and clippings in the bin before making her way to the door.

"I'll leave you two alone so you can have your talk. But if you get into another fist fight, you're on your own. Don't coming running back to me to dab at your wounds." She said as she eyed each man individually before stepping out.

Jonathan took in a deep breath as he waited for the bomb to explode.

"I'm sorry." John said in a whisper so soft Jonathan almost thought he had imagined it.

The biotic looked up, eyes wide. John chuckled.

"Unexpected?"

"Well… yeah." Jonathan said incredulously.

John was still smiling.

"I thought so too." He said shaking his head before folding his arms and walking slowly towards his double.

"Listen… I may have been a bit harsh towards you since we found you."

Jonathan snorted.

"Ok, maybe more than just a little." John sighed before continuing, "Truth is I was so caught off guard that I fell back into my 'survival mode' where I turn in to a complete asshole. It's kinda like a reflex, I guess."

Jonathan didn't say anything; he just sat there regarding the man in front of him for a while.

"Liara put you up to this, didn't she?" he asked with a raised eyebrow as he folded his arms.

John looked momentarily surprised at being caught out. He smiled and kicked at an invisible pebble.

"Guess I should know better than to try and pull the wool over my own eyes."

Jonathan tilted his head to the side as he waited for John to continue.

"She did suggest that I come here and try to smooth things over, yes."

"Thought so." Jonathan said nodding to himself.

"So what did Liara tell you to tell me?"

"Hey it's not like that. She only asked me to come here, what I've said to you has been my own words."

Jonathan regarded him for a moment before sighing.

"Ok, I believe you. You were saying how you are an asshole when you're caught off guard."

"Yes, well… I shouldn't have been such a dick. I kind of know what you're going through. Not exactly, I know, but to a certain extent. After the Collector attack I was basically stone cold dead. It took Cerberus two years to rebuild my mind and body. I guess at the same time they started on me they began working on you too."

Jonathan sat quietly listening to what John was saying. He noticed that it seemed as if John was forcing himself to carry on. Like he didn't want to delve into those memories again.

"When I woke up two years of my life were gone. I was surrounded by people I didn't know, working for what most people considered to be a terrorist organization. My friends and family thought me dead. Most of them had moved on. I felt so alone." John said in a quite voice.

Jonathan didn't know how to react. John was showing a completely different side of himself, a vulnerable side that he hid from the world. Jonathan was surprised that he was being so open, especially to him. He wondered if he had spoken to Liara or even Kaidan like this before. Something inside told him that was highly unlikely.

John cleared his throat before continuing.

"About three months after my revival, the Illusive Man sent us to look into a human colony on Horizon. We had determined that Horizon was to be the Collector's next target. We arrived just as the Collectors attacked. It took a lot of effort but in the end we were able to drive them off the planet by hacking the AA guns that served as the colonies defenses."

"Go on" Jonathan urged.

"As we were about to leave, Kaidan appeared. He had been assigned by the Alliance to upgrade the defenses on Horizon. He was one of the few to escape being taken by the Collectors."

John paused a moment before speaking again.

"I was so happy to see him. I thought he would be glad to see me too but that wasn't the case. At least it didn't appear so."

"What happened?"

"Kaidan was furious. He couldn't believe I was alive and hadn't contacted him. The fact that I was with Cerberus only made it worse. He called me a traitor to the Alliance and refused to let me explain. I could feel a light inside my heart go out. All I had been thinking of for those past months was that I wanted to see him again. To tell him how I really felt. Dying really opens your eyes to such things, you know?" John said with a sigh, pressing his thumb and finger to his temples.

"Anyway… Soon after that I ran into Liara again on Illium. I guess I latched on to her. We grew close. Slowly, Kaidan started to fade into the back of my mind. We completed our mission, destroying the Collector base and turning our backs on Cerberus. After that came the Batarian incident, followed by my grounding. I was on Earth for about six months when the Reapers attacked. It was on that day that I saw Kaidan again and everything just came rushing back. And with all the death and destruction, the weight of the whole galaxy and my relationship with Liara… Things just became too complicated and when Kaidan came out and told me he had feelings I panicked. The look of rejection on his face broke me all over again…"

Jonathan couldn't meet the eyes of the man before him. He felt bad for judging him these past few days. Now he thought he understood why John acted the way he did. It was all a front to hide what was actually killing him inside. For all his bravado and egotistical mannerisms he was actually just a plain human being. In a way Jonathan knew what he felt like. He had experienced the pressure of leadership when going up against Saren and Sovereign, John had been through so much more while Jonathan had been floating in a tank. He felt deeply sorry for this man.

"What I'm getting at is that I rejected Kaidan. I pushed him away. So I have no right to take it out on you now that he has found someone else." John looked at his boots as he finished.

"I'm sorry, John. I hadn't really considered all that could have happened to you in the past. Honestly I thought you were just being a jealous prick."

Both men chuckled softly.

"I'm not going to end it though." Jonathan said firmly.

John looked up to meet the solid stare.

"The way you feel about him is exactly how I feel. I'm a clone of you after all. I'm not giving up on him. On us."

John stared at him a moment before sadly smiling.

"Yeah, didn't think you will. I wouldn't have."

It was silent in the Med bay for a few minutes before either spoke.

"What are you gonna do now?"

John sighed.

"Well, I'm going to go have a honest talk with Liara. It's not fair that I hide my feelings from her. She has to know that I still care for him. We'll see where it goes from there."

Jonathan nodded.

"That would be best I think."

"I should also speak to Kaidan. Apologize to him as well."

Jonathan stood.

"I'll tell him you're looking for him."

John nodded and stepped to the side to let the other man pass.

Just before he reached the door, Jonathan turned back.

"Thank you for telling me everything. I know it couldn't have been easy.'

"Thank you for listening. I guess it's better to talk to someone about it. Even if it means talking to yourself." He said with a small smile.

Jonathan smiled back but it was a forced smile.

"Listen," John said, noticing the look on Jonathans face. "Even though you aren't the Commander of your own ship anymore, you're still a Shepard. And we could really use your help in this fight."

Jonathan smiled again, this time it was a real smile.

"At your service, Commander." Jonathan said, saluting the man standing across from him.

John smiled too and saluted back.

Jonathan turned once more towards the door but was stopped by a hand on his shoulder.

"If you speak of this to anyone, I'll deny it. It never happened, got it? I have my reputation to uphold after all."

Jonathan smiled to himself and shook his head as the shell re-formed around the man who had moments ago bared his soul.

"In that case Commander, you should disable the comm-system next time." came Jokers voice over the intercom.

John's face went bright red. Jonathan burst out laughing.

"You'd better get that brittle ass of yours behind some cover Joker, because when I get my hands on you…!" John yelled as he stormed off, probably to got throttle the pilot.

* * *

Jonathan slowly made his way towards the lounge where Kaidan usually hung out when they had down time, chuckling as he moved along. He was glad that at least some of the tension had been worked out. He had no doubts that this wasn't the end of the issue, but for now at least things were ok.

He found Kaidan staring out at the endless emptiness of space, his back turned to the door.

"What did Joker do this time?" the Major asked, turning around to face him.

"He was eavesdropping."

Kaidan snorted.

"I'm not surprised. On who?"

"Us. John and me."

"You spoke to him? " Kaidan asked, his brows lifting in surprised.

"Yep. It was quite informative. He wants to speak to you as well when he has the chance."

Kaidan sighed.

"I guess it would be best to talk it out." He said looking back out into space.

"What did he say? About 'us' I mean?"

Jonathan liked the way he said 'us'. He smiled briefly before answering.

"Well, basically he said he was sorry for the way he has been acting. He was just feeling overwhelmed and then the two of us together kinda sent him over the edge."

"I see."

"So now what?"

"What do you mean?" Kaidan asked.

"Do we give 'us' a go?"

Kaidan tilted his head and folded his arms.

"Are you willing to settle for a copy?" Jonathan asked in a small voice.

Kaidan's eyes widened. He walked forward and took Jonathan's hands.

"Don't you dare say that!"

"But it's true." Jonathan said.

"Jonathan, you aren't a copy. You're your own person. And…"

"And?"

"And you're real enough for me." Kaidan said and placed his hand on Jonathan's cheek.

Jonathan smiled and leaned forward. As their lips met, time seemed to stand still. Jonathan lost himself in the embrace until they finally broke apart for air. Jonathan drew him close in a tight hug.

"Thank you." He whispered as he buried his face in the crook of Kaidan's neck.

Kaidan hugged him tighter as he felt the tears seeping through his shirt onto his shoulder.

* * *

**So crisis averted for now, but don't worry, there will still be a few juicy rivalry scenes in the future ;) Maybe even a... threesome *nudge nudge* We'll have to see where it goes.**

**I know it seems quite strange that Kaidan has turned away from John so fast but all will be explained and elaborated upon in chapters to come. Up next is John's chats with both Liara and Kaidan so expect more emotional scenes. After that the story can get going. There are Reapers to defeat after all...**

**Any questions/suggestions? Feel free to speak up.**

**Thanx for all the feedback so far, it really makes a difference :)**


	7. Chapter 7

**Ok so this chapter might be a bit random and not entirely sensible, but thats probably because I've had a bit to drink...**

**I decided that in honour of the latest dlc and the various similarities between it and this fic (I was completely unaware of the 'clone' thing until 'Sculla' made a comment about it a few days ago) that I would post an update. It's about time as well, I guess.**

**Anyway, enjoy ;) And be warned, there is some level of steaminess towards the end of this chapter so if you don't like... I did warn you...**

* * *

Liara was in her room, tapping away at one of the many screens as usual. John drew in a deep breath as he stepped inside. He knew this conversation had the potential to go horribly wrong, but he also knew that it had to happen. It would be a greater wrong to keep quiet about the way he felt.

"Shepard, how did it go?" the Asari asked as she saw him enter.

John rubbed at the back of his neck.

"It was… awkward, to say the least. But overall not that bad, I guess."

"I see. That's good, right?"

"Yeah, suppose it is."

Liara stood and walked over to him, placing her hands on his chest and leaning in to kiss him. John turned his head away just before their lips touched. The Asari pulled back, confusion in her eyes.

"What's wrong?"

John sighed and looked from her face to the floor.

"We have to talk, Liara." He said softly.

The Asari took a step back.

"Ok. What do you want to talk about?"

"Well, 'us' for one." He said and walked over to lean against a wall.

"I see…"

"Look, I haven't been completely honest with you. I never thought It would turn out this way so I didn't think it mattered that much, but now-"

"You still care for him, don't you?" Liara interrupted, catching John a little off-guard.

For a moment John didn't know how to respond. He stood there dumbly, not entirely sure what to say.

"How long have you known?"

"Oh come on, John. It's quite clear, the way you've been acting lately. You're jealous of Jonathan."

"I- I didn't think it was that obvious…"

Liara walked over to where he stood and took his hands.

"Shepard, I can't change the way you feel. If you'd rather be with someone else…"

"Liara stop. Part of why I didn't say anything sooner was because I had grown to care about you in a very deep way. It's not the same as the way I feel about Kaidan, but it is just as strong."

John paused for a moment, looking into her bright blue eyes.

"Listen I know it sounds strange, but I don't know how to explain it… I care about you both and I don't want to loose either of you…" John whispered, his voice cracking with emotion.

The pain Liara saw in his eyes made her heart ache. She reached up with her hand and stroked his cheek. He leaned into the touch.

"Shepard, I think I understand how you feel, but… You can't have us both. You'll have to make a choice and you'll have to do it on your own. I'm not going to tell you to choose me. You have to do what your heart tells you to." She said and pulled his head down to place a kiss on his cheek.

Shepard stood staring at her for a moment as she backed away, moving to the console she had been working at earlier.

"Now, I have some work to get back to." She said and turned away.

Shepard slowly made his way to the door, his mind in a far away place. He didn't look back as he stepped through the entrance. If he had, he would have seen a tear roll down a blue cheek.

* * *

After about half an hour of silent contemplation John decided to go and find Kaidan. He checked the CIC, Mess, Crew Quarters and the Lounge but found no sign of the biotic. Last place left to look was the Observation Deck. As he crossed the hallway towards the door, he thought about what he was going to say exactly. He had been thinking about it for some time now, but as the moment approached his mind was all fuddled. He sighed and pressed his hand against the access panel. With a quite hiss the door slid open. John drew in a sharp breath as he stepped inside.

On the couch lay Jonathan. He was asleep, a data pad held loosely in his one hand. His other arm was wrapped around a sleeping Kaidan who lay next to him, his hand and leg draped over Jonathan's body. John was momentarily shocked. He stood staring at the scene before him for what felt like hours even though only a few seconds had passed. Kaidan stirred in his sleep, wrapping his arm around Jonathan and pulling him a bit closer. The man smiled slightly in his sleep and buried his face in Jonathan's chest.

John looked on for a few more moments before turning to leave. Strangely he felt no jealousy or anger as he had expected to. His mind was suddenly quite clear. He could not come between the two of them now. He had screwed it up. He smiled slightly as he glanced back for a second. They looked so peaceful together. He imagined what it would be like to be there in Jonathan's place. He savored that feeling for a moment before finally letting it go. As he walked away he let his emotions slip, pushing his love for Kaidan back into the darkness.

Liara turned in surprise as the door to her room slid open once more.

"Shepard, what's wrong?" she asked and walked over to him. She studied the look on his face, unsure of what she saw there.

"Did you speak to Kaidan? What did he-" she began but was interrupted when John suddenly grabbed her and pulled her into a passionate kiss.

"It's you, Liara. I choose you." He breathed and kissed her down the side of her neck.

Liara was both confused and overjoyed at the same time. She wanted to ask him about it, but the way his mouth was moving across her neck made her shiver with desire. She groaned as his tongue darted out to leave a searing trail on her skin. All protests forgotten she grabbed him by the shoulders and pushed him towards the bed. The two of them furiously worked at removing their clothes as they stumbled towards it. Finally when both stood naked they grabbed at each other again, their bodies colliding in pleasure. As they fell back onto the bed, Liara thought she saw something odd in Shepard's eyes but she brushed it away as he leaned in to capture one of her breasts with his lips. She moaned in ecstasy. It was going to be a long night and she was going to make sure she enjoyed it. She would worry about everything else later.

* * *

_A few moments earlier…_

Kaidan's eyes opened as he heard the door close with a click. He lifted his head slightly and glanced around. When he saw no one else in the room he guessed that who ever had been there had just left. He lay his head back down and smiled at the warmth that radiated off of Jonathan's body. He moved his hand to stroke Jonathan's chest but stopped when he ran into an 'obstacle'. Lifting his head once more he saw that his hand was resting on Jonathan's crotch and by the looks of it Jonathan wasn't finding it at all an unpleasant situation. Kaidan's face flushed with embarrassment for a moment before an entirely different emotion settled in. He felt his own pants tighten a bit as his mind drank in the possibilities.

On impulse he leaned up and kissed Jonathan tendely. The clone's eyes opened with a slight flutter. It only took him a moment to process what was going on and soon he was kissing Kaidan back with equal passion. The data pad hit the floor with a thud but neither man made any move to retrieve it. Kaidan moved to sit up and straddle Jonathan. In a swift movement he pulled off his shirt and reached down to dispose of Jonathan's as well. The feeling of bare skin against skin sent jolts of pleasure through them, driving them to kiss and touch with more intensity.

After a few minutes of pure bliss, Jonathan pushed Kaidan back and stood up. Before Kaidan could protest he had his hands at the biotic's waist and set about working the buckle loose. Moments later Kaidan felt a shiver run through him as the cool air hit his arousal. Jonathan grinned at him slyly before running his tongue from the base of Kaidan's member to the sensitive tip. Kaidan groaned loudly at the wet warmth that closed in around him, throwing his head back. For a brief moment he thought that maybe this wasn't the right time for this but as soon as the idea crossed his mind it was out again, thanks to Jonathan's wicked lips. He decided then that he would fret about it later. For now he planned on getting lost in the ecstasy that was Jonathan Shepard.

* * *

"Joker, I am detecting unsually high levels of pheromones in two places on the ship."

The pilot looked over at the AI.

"Where's Shepard? And uh Shepard?" he asked.

EDI paused for a moment, obviously scanning the Normandy.

"My sensors indicate that both are present at the epicenters of each phenomena respectively." She said.

Joker thought a moment before smiling.

"Are there any other crew members with them?"

"Yes," the AI replied, "Sensors show that both Liara and Kaidan are involved."

Jokers smile widened and he chuckled to himself.

"Hey EDI, could you maybe bring up the surveillance footage?" he asked with a cheeky grin.

"Why?" the AI asked, looking confused.

"To get some pointers of course."

* * *

**Ok so some of you might freak out about what has happened so far, but be patient and bare with me... Not everything is set in stone and things may turn out quite differently than you think.**

**Thanx for reading and thanx for all the reviews and faves. It really does motivate me to keep writing ;)**

**Till next time...**


	8. Chapter 8

**Short little update because I had some time to kill. Basically just a little aftermath situation. Next chap will probably follow soon, within a week or so (hopefully)**

* * *

"Kaidan? Kaidan?! Get up!" the voice called over the comm system.

The biotic groaned and rubbed at his eyes. Leaning up on one arm he glanced around. He was on the floor of the Observation Deck, tangled up in a pile of clothes. His eyes widened as he remembered the previous night. His surprise was swiftly replaced with giddy satisfaction. It had been amazing.

Deep breathing nearby made him turn around. Jonathan was fast asleep on the couch, his arm hanging off the side. A shirt was loosely draped over him to cover some of his nakedness. Kaidan grinned at the contented smile that was on the sleeping man's face. Looking down Kaidan saw he was also still naked. On his chest he noticed an odd sheen. Momentarily confused he rubbed his hand across it. It was slightly sticky. A jolt ran through him as he realized exactly what it was. His face flushed red.

"Kaidan? You finally awake?" the voice asked, making Kaidan jump. Kaidan recognized it as Joker.

"Yeah, what's up?" Kaidan asked, his voice sounding a bit hoarse. He wasn't really surprised.

"The Commander wants you to suit up. ETA 20 minutes."

"Alright. On my way." He said, looking longingly at the sleeping figure. He didn't want to leave.

"Jonathan has to get ready too." Joker added.

Kaidan looked surprised.

"What? Really? John asked for him too?"

"Yep." The pilot replied. "You both have to meet him and Garrus in the shuttle bay in well, about fifteen minutes."

"Alright." Kaidan said, still a bit taken aback. He stood and gently nudged Jonathan's shoulder. The sleeping man stirred before slowly opening his eyes.

"Hey." He said with a sleepy smile.

Kaidan leaned in and kissed him tenderly.

"Get up. We've got to get ready." He said as he moved to sift through the pile of clothes to find his pants.

"For what?" Jonathan asked sitting up.

"John needs us for a field mission."

Jonathan's eyes widened slightly.

"He asked for me?"

"Yep. Surprising, isn't it?"

"A bit. I guess we're starting to get along better now." Jonathan said, pulling Kaidan closer. He kissed him across his chest, grinning, as he tasted the saltiness there.

"Guess we were a bit messy."

"Just a bit." Kaidan said with a grin as he pulled away to finish putting on his clothes. They smelled a bit musky but he didn't have time to worry about that.

"We can take a hot shower when we get back."

Jonathan grinned.

"Looking forward to it." He said in a voice that made Kaidan want to jump him. If it weren't for the mission he might have done just that.

Moments later both were half presentable and so they swiftly made their way to the armory. Neither John nor Garrus were there yet, which Kaidan thought was odd but he quickly busied himself with suiting up. Minutes later both biotics were armed and ready.

"Maybe I should wear my helmet." Jonathan said softly.

"Why? As far as I know it's a planetary mission with breathable atmosphere. You don't need it."

"I think I do. It would be easier if no one could see my face. It might raise some suspicions if people saw the two of us, John and I, together. I don't think John needs that kind of attention right now. He's got enough on his mind." Jonathan said and picked up the helmet that lay before him.

Kaidan blinked in surprise at the compassion in Jonathan's voice. It made him smile.

"You really are quite amazing." He whispered, making the clone look up at him, a slight red tinge on his cheeks.

Kaidan reached out and grabbed his arm, pulling him close.

"Well, seeing as the others are late…" he said, grinning suggestively.

Jonathan chuckled before leaning in to kiss Kaidan. Just as their lips met, someone cleared their throat loudly. Both men spun to see Garrus leaning against the table; a crooked smile on is face.

"So you two were the ones making all that noise last night?" he asked, laughing as the two humans went red in the face.

Before anyone could say anything, Shepard stepped out of the elevator. He was already dressed in his armor, his guns strapped to his back. Cortez stepped out behind him, followed by Vega.

"Glad to see everyone's ready." The Commander said simply and strode over to the shuttle. Cortez got in with him, the Kodiac powering up moments later. Vega winked at Kaidan as he passed by on his way to his usual spot.

"Walked into the Obsevation Deck this morning. Looked like you two had a great time." He said with a chuckle, making the two of them go an even deeper shade of red and Garrus burst out laughing.

"Hey, what's going on out there? Let's go!" Shepard called from the shuttle.

Vega chuckled again and turned to walk away while the other three turned towards the shuttle door.

"What's up with you two?" John asked as the two red faced men stepped aboard.

"Nothing." Kaidan said, not making eye contact. Jonathan kept quiet and pulled on his helmet. John noticed this but said nothing.

"Alright then. Take us away, Cortez."

* * *

**So, it's a bit random...**

**I know they're acting like horny teenagers, but honestly, if you had either of them wouldn't you want to be all over them all the time too?**

**Any requests/suggestions for future chapters? What mission do you want them to go on? After this part I want to do the Thessia mission and then its on to Sanctuary and the Cerberus base.**

**Thanx for reading :)**


End file.
